How do you restart the process? Try deleting the [xc]/var directory and then open the "admin.php" script in your browser (i.e. the back end, not the storefront - opening the storefront won't start the cache rebuilding process). Does this help?

The first thing you need to do with your custom modules is
1) Find their Main.php files
2) Change getMajorVerion() method there, so it would return 5.1 instead of 5.0. After next cache rebuild, you will be able to use them.